[Bioperl-l] Re: GFF3

[Jason Stajich]

test count was off.
1..19
[SNIP]
ok 20
ok 21
ok 22

You can also try
% make test_FeatureIO
to run just a specific test within the test framework to look at things.

Fixed.
On Jan 19, 2005, at 6:30 PM, Scott Cain wrote:

> Weird: when I run the FeatureIO test on the command line (via `perl
> t/FeatureIO.t`), all tests pass.  When I run it as part of 'make test',
> tests 20-22 fail.  Does anyone know why that sort of thing might  
> happen?
>
> thanks,
> Scott
>
> ----------------------------------------------------------------------
> Scott Cain, Ph. D.				 	 cain at cshl.org
> GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
> ----------------------------------------------------------------------
>
>
> On Wed, 19 Jan 2005, Allen Day wrote:
>
>> okay, let me know.  we should probably add some validation tests as  
>> well,
>> right now i'm just making sure the lines can be processed but don't  
>> do any
>> typechecking on the document.
>>
>> Rob, would you mind writing some tests into FeatureIO.t for your
>> validation code?
>>
>> -allen
>>
>>
>> On Wed, 19 Jan 2005, Scott Cain wrote:
>>
>>> I just did a cvs update and the last few tests are failing on MacOSX  
>>> 10.3.
>>> I'll try to sort it out over the next couple of days.
>>>
>>> Scott
>>>
>>> --------------------------------------------------------------------- 
>>> -
>>> Scott Cain, Ph. D.				 	 cain at cshl.org
>>> GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
>>> --------------------------------------------------------------------- 
>>> -
>>>
>>>
>>> On Tue, 18 Jan 2005, Allen Day wrote:
>>>
>>>>> The first series of errors die because the feature ID=AB000114 in
>>>>> t/data/knownGene.gff3 has several Dbxrefs separated with ';'  
>>>>> instead of
>>>>> ','
>>>>
>>>> i'm not getting these errors, are you are in sync with cvs HEAD?
>>>>
>>>>> The second failure is because  hybrid1.gff3 isn't in cvs
>>>>
>>>> gff files are in cvs now.
>>>>
>>>>>
>>>>> Rob
>>>>>
>>>>>
>>>>>
>>>>> % perl -I. -w t/FeatureIO.t
>>>>> 1..19
>>>>> ok 1
>>>>> ok 2
>>>>> ok 3
>>>>> ok 4
>>>>> ok 5
>>>>> ok 6
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
>>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
>>>>> 593,
>>>>> <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
>>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
>>>>> 593,
>>>>> <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
>>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
>>>>> 593,
>>>>> <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
>>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
>>>>> 593,
>>>>> <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
>>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
>>>>> 593,
>>>>> <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
>>>>> Use of uninitialized value in substitution (s///) at
>>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
>>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
>>>>> 593,
>>>>> <GEN5> line 10.
>>>>> ok 7
>>>>> ok 8
>>>>>
>>>>> ------------- EXCEPTION  -------------
>>>>> MSG: Could not open t/data/hybrid1.gff3: No such file or directory
>>>>> STACK Bio::Root::IO::_initialize_io Bio/Root/IO.pm:314
>>>>> STACK Bio::FeatureIO::_initialize Bio/FeatureIO.pm:345
>>>>> STACK Bio::FeatureIO::gff::_initialize Bio/FeatureIO/gff.pm:92
>>>>> STACK Bio::FeatureIO::new Bio/FeatureIO.pm:268
>>>>> STACK Bio::FeatureIO::new Bio/FeatureIO.pm:288
>>>>> STACK toplevel t/FeatureIO.t:83
>>>>>
>>>>> --------------------------------------
>>>>>
>>>>
>>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/